LAMMPS (4 Nov 2022)
# 35,000 atom nylon melt example

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

read_data large_nylon_melt.data.gz   extra/bond/per/atom 5    extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
Reading data file ...
  orthogonal box = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648)
  2 by 1 by 2 MPI processor grid
  reading atom labelmap ...
  reading bond labelmap ...
  reading angle labelmap ...
  reading dihedral labelmap ...
  reading improper labelmap ...
  reading atoms ...
  35200 atoms
  reading velocities ...
  35200 velocities
  scanning bonds ...
  9 = max bonds/atom
  scanning angles ...
  21 = max angles/atom
  scanning dihedrals ...
  31 = max dihedrals/atom
  scanning impropers ...
  29 = max impropers/atom
  reading bonds ...
  33600 bonds
  reading angles ...
  59200 angles
  reading dihedrals ...
  80000 dihedrals
  reading impropers ...
  35200 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    12 = max # of 1-4 neighbors
    41 = max # of special neighbors
  special bonds CPU = 0.007 seconds
  read_data CPU = 0.854 seconds

velocity all create 800.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
  1 molecules
  0 fragments
  18 atoms with max type 8
  16 bonds with max type 12
  25 angles with max type 24
  23 dihedrals with max type 33
  2 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
  1 molecules
  0 fragments
  18 atoms with max type 9
  17 bonds with max type 11
  31 angles with max type 23
  39 dihedrals with max type 30
  0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
  1 molecules
  0 fragments
  15 atoms with max type 9
  14 bonds with max type 11
  25 angles with max type 23
  30 dihedrals with max type 30
  0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
  1 molecules
  0 fragments
  15 atoms with max type 11
  13 bonds with max type 13
  19 angles with max type 25
  16 dihedrals with max type 29
  2 impropers with max type 11

thermo 50

# dump 1 all xyz 100 test_vis.xyz

fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

# stable at 800K
fix 1 statted_grp_REACT nvt temp 800 800 100

# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1

thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts

# restart 100 restart1 restart2

run 200

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012

@Article{Gissinger17,
 author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
 title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
 journal = {Polymer},
 year =    2017,
 volume =  128,
 pages =   {211--217}
}

@Article{Gissinger20,
 author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
 title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
 journal = {Macromolecules},
 year =    2020,
 volume =  53,
 number =  22,
 pages =   {9953--9961}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
  G vector (1/distance) = 0.20765034
  grid = 18 18 18
  stencil order = 5
  estimated absolute RMS force accuracy = 0.033315619
  estimated relative force accuracy = 0.000100329
  using double precision KISS FFT
  3d grid and FFT values/proc = 4508 1620
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.5
  ghost atom cutoff = 10.5
  binsize = 5.25, bins = 15 15 15
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) fix bond/react, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 81.39 | 81.41 | 81.43 Mbytes
   Step          Temp          Press         Density      f_myrxns[1]    f_myrxns[2]  
         0   800            3666.3948      0.80366765     0              0            
        50   673.94821     -9679.5038      0.80366765     31             0            
       100   694.36354     -2108.4881      0.80366765     57             22           
       150   716.5075      -12356.04       0.80366765     77             50           
       200   722.97306     -1308.3439      0.80366765     84             67           
Loop time of 23.1041 on 4 procs for 200 steps with 35200 atoms

Performance: 0.748 ns/day, 32.089 hours/ns, 8.656 timesteps/s, 304.708 katom-step/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 6.6935     | 6.8618     | 7.0049     |   5.1 | 29.70
Bond    | 3.8936     | 3.9807     | 4.0626     |   3.5 | 17.23
Kspace  | 1.1828     | 1.4033     | 1.6503     |  16.6 |  6.07
Neigh   | 8.7942     | 8.7945     | 8.7946     |   0.0 | 38.06
Comm    | 0.14682    | 0.15559    | 0.16441    |   1.8 |  0.67
Output  | 0.00035959 | 0.00037472 | 0.00041627 |   0.0 |  0.00
Modify  | 1.8787     | 1.8787     | 1.8788     |   0.0 |  8.13
Other   |            | 0.02917    |            |       |  0.13

Nlocal:           8800 ave        8911 max        8662 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost:        18358.5 ave       18438 max       18183 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Neighs:    1.73191e+06 ave 1.77313e+06 max 1.68375e+06 min
Histogram: 1 0 1 0 0 0 0 0 0 2

Total # of neighbors = 6927655
Ave neighs/atom = 196.80838
Ave special neighs/atom = 9.8480114
Neighbor list builds = 128
Dangerous builds = 0

# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:24
